pipelines.chromake.scripts.config

pipelines.chromake.scripts.config

The config module of chromake contains functions to read and write the config file of the chromake pipeline.

Functions

Name	Description
check_config_format	Check the configuration file to make sure it follow the requirements of chromake. At runtile, it will stop snakemake if the file format is invalid.
check_project_and_sequencing	Ensures that projects with no associated sequencing samples are removed from the config, and removes empty sequencing projects, while making sure the mark is considered in the filtering process.
check_sample_files_exist	Check if all R1 and R2 FASTQ files listed in the config exist.
create_config_from_table	Create a YAML config from a table. Supports SAMPLES and optional INPUT files.
create_example_config	Create an example genomake/chromake YAML configuration file.
create_samplesheet_from_config	Create a samplesheet table (CSV or Excel) from a YAML config, resolving relative paths
remove_samples	Remove specific samples from a project in the YAML config.
remove_sequencing	Remove an entire sequencing project from the YAML config.
update_jobs	Update or add the JOBS section in an existing YAML config.

check_config_format

pipelines.chromake.scripts.config.check_config_format(cfg, raise_error=True)

Check the configuration file to make sure it follow the requirements of chromake. At runtile, it will stop snakemake if the file format is invalid.

Parameters

Name	Type	Description	Default
cfg	dict	A dict object representing a configuration file for the chromake pipeline.	required
raise_error	bool	Raise a runtime error or simply print the message.	True

check_project_and_sequencing

pipelines.chromake.scripts.config.check_project_and_sequencing(config)

Ensures that projects with no associated sequencing samples are removed from the config, and removes empty sequencing projects, while making sure the mark is considered in the filtering process.

Parameters

Name	Type	Description	Default
config	dict	Loaded YAML config (as a dictionary).	required

Returns

Name	Type	Description
	dict	Updated config dictionary.

check_sample_files_exist

pipelines.chromake.scripts.config.check_sample_files_exist(config_path)

Check if all R1 and R2 FASTQ files listed in the config exist.

Parameters

Name	Type	Description	Default
config_path	str	Path to the YAML config file.	required

Returns

Name	Type	Description
	bool	True if all R1 and R2 files exist, False otherwise.

create_config_from_table

pipelines.chromake.scripts.config.create_config_from_table(
    table_path,
    output_path,
    proj_paths,
    jobs=None,
    sequencings=None,
)

Create a YAML config from a table. Supports SAMPLES and optional INPUT files.

Parameters

Name	Type	Description	Default
table_path	str	Path to the input CSV or Excel table.	required
output_path	str	Path to write the YAML config.	required
proj_paths	dict	Dictionary of project_name -> project_path.	required
jobs	dict	Default JOBS settings (CORES_PER_JOBS, QOS_INFOS).	None
sequencings	dict	Dictionary of sequencings informations (PATH, R1_ADAPTOR, R2_ADAPTOR).	None

Returns

Name	Type	Description
	str	Path to the written YAML config file.

create_example_config

pipelines.chromake.scripts.config.create_example_config(
    filename='test_config.yaml',
)

Create an example genomake/chromake YAML configuration file.

Parameters

Name	Type	Description	Default
filename	str	Filename to use if output is a directory.	'test_config.yaml'

Returns

Name	Type	Description
	str	Path to the written YAML configuration file.

create_samplesheet_from_config

pipelines.chromake.scripts.config.create_samplesheet_from_config(
    config_path,
    output_path,
    strand_columns=False,
    excel=True,
)

Create a samplesheet table (CSV or Excel) from a YAML config, resolving relative paths by adding the sequencing project path. Includes both SAMPLES and INPUTS.

Parameters

Name	Type	Description	Default
config_path	str	Path to the YAML config file.	required
output_path	str	Path to save the generated table (CSV by default; Excel if excel=True).	required
strand_columns	bool	If True, each strand (R1, R2) PATH will be a separate column (wide format); if False, each strand will be in separate rows and a STRAND columns will be added to differentiate them (long format).	False
excel	bool	If True, save as Excel (.xlsx). Otherwise, save as CSV.	True

Returns

Name	Type	Description
	str	Path to the generated samplesheet file.

remove_samples

pipelines.chromake.scripts.config.remove_samples(
    config_path,
    sequencing_name,
    samples,
)

Remove specific samples from a project in the YAML config.

Parameters

Name	Type	Description	Default
config_path	str	Path to the YAML config file.	required
sequencing_name	str	Name of the project containing the samples.	required
samples	list of str	List of sample names to remove.	required

remove_sequencing

pipelines.chromake.scripts.config.remove_sequencing(
    config_path,
    sequencing_name,
)

Remove an entire sequencing project from the YAML config.

Parameters

Name	Type	Description	Default
config_path	str	Path to the YAML config file.	required
sequencing_name	str	Name of the sequencing project to remove.	required

update_jobs

pipelines.chromake.scripts.config.update_jobs(config_path, jobs)

Update or add the JOBS section in an existing YAML config.

CORES_PER_JOBS: number of cpu cores to use for each jobs (>=1)

QOS_INFOS: if using an executor like slurm, indicate the name of the qos (e.g. short), and the associated MaxWall in minutes.

Parameters

Name	Type	Description	Default
config_path	str	Path to the YAML config file.	required
jobs	dict	Dictionary containing JOBS information to update. Can be a full replacement or partial update.	required

Example

jobs_update = {
    "CORES_PER_JOBS": {
        "FASTQC": 10,
        "CUTADAPT": 10,
        "BOWTIE2": 30,
        "SAMTOOLS_QC": 5,
        "MULTIBAMSUMMARY": 5,
        "BEDTOOLS": 5
    },
    "QOS_INFOS": {
        "short": {"MaxWall": 2000},
        "medium": {"MaxWall": 5000},
        "long": {"MaxWall": 15000} 
    }
}
update_jobs("config.yaml", jobs_update)